BN1578 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.0327e-05 2.2717e-04
Layer 5 1.8459e-05 1.1490e-03
Layer 3 4.4801e-04 6.8648e-02
Layer 6 9.9554e-04 3.7493e-03
Layer 2 7.7634e-02 2.2975e-01
Layer 1 8.3908e-01 6.9054e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.6016 0.7268
HPCA Layer 4 3.0645 0.7225
EFHD2 Layer 4 2.3213 0.7171
MOAP1 Layer 5 2.5176 0.7165
QDPR Layer 4 2.4453 0.7129
FKBP8 Layer 4 2.5508 0.7070
SEZ6L2 Layer 5 2.2930 0.6973
SNAP91 Layer 4 2.3125 0.6952
NUDT4 Layer 5 2.4727 0.6947
MGST3 Layer 6 2.4121 0.6935
SLC25A22 Layer 5 2.5566 0.6902
GOT1 Layer 5 2.3242 0.6893
SULT4A1 Layer 4 2.7129 0.6885
SYN2 Layer 5 2.6719 0.6825
REEP5 Layer 4 2.4863 0.6819
CHGA Layer 4 2.6836 0.6803
TTC9B Layer 5 2.8369 0.6797
CPLX1 Layer 5 2.3926 0.6776
CAPNS1 Layer 5 2.4453 0.6775
B4GAT1 Layer 5 2.4023 0.6771
TUBA4A Layer 5 2.4541 0.6759
TAGLN3 Layer 6 2.4121 0.6756
G3BP2 Layer 4 2.5215 0.6754
HINT1 Layer 4 2.2168 0.6753
DNAJC6 Layer 5 2.3184 0.6747
TUBB2A Layer 5 2.2578 0.6741
SYP Layer 5 2.5537 0.6732
APBB1 Layer 4 2.4121 0.6726
PSMB5 Layer 5 2.1250 0.6721
CTSD Layer 5 2.5566 0.6719
NRSN1 Layer 4 2.4512 0.6718
SATB1 Layer 4 2.5029 0.6717
SEPTIN4 Layer 6 2.3027 0.6715
PIN1 Layer 5 2.4941 0.6712
CLDND1 Layer 6 2.4297 0.6711
ITPK1 Layer 4 2.5195 0.6708
STMN2 Layer 5 2.4180 0.6705
STX1B Layer 4 2.5303 0.6702
SLC24A2 Layer 5 2.5215 0.6692
DBNDD2 Layer 6 2.6074 0.6691
SH3GL2 Layer 6 2.7598 0.6681
ATP6V1B2 Layer 4 2.5215 0.6681
MAPK8IP2 Layer 4 2.4844 0.6673
HCFC1R1 Layer 4 2.3994 0.6671
CAMK2G Layer 4 2.4785 0.6670
SPOCK1 Layer 4 2.5664 0.6670
NAP1L5 Layer 5 2.4844 0.6663
PRUNE2 Layer 4 2.4238 0.6655
CRYAB Layer 6 2.3340 0.6641
WBP2 Layer 6 2.2617 0.6639

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1578
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1578_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1578/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1578/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1578/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1578/report/PD/BN1578_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1578/report/PD/BN1578_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 05:18:35
  • Number of Processes: 10
  • Spending Time: 0h 3m